Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate GFF2541 Psest_2591 3-isopropylmalate dehydratase, large subunit
Query= CharProtDB::CH_024771 (466 letters) >FitnessBrowser__psRCH2:GFF2541 Length = 475 Score = 607 bits (1564), Expect = e-178 Identities = 308/470 (65%), Positives = 366/470 (77%), Gaps = 8/470 (1%) Query: 3 KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62 KTLY+KL++ H V ++ + L+YIDRH++HEVTSPQAF+GLR R + AT D Sbjct: 4 KTLYDKLWEMHEVKRRDDGSSLIYIDRHILHEVTSPQAFEGLRLANRKPWRIDANIATPD 63 Query: 63 HNVSTQTKDINACG------EMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQG 116 HNV T TK G E++RIQ+Q L +NC +FG+ + +N QGIVHV+GPEQG Sbjct: 64 HNVPT-TKGERQGGLEAIADEVSRIQVQTLDENCDDFGILEFKMNDVRQGIVHVIGPEQG 122 Query: 117 VTLPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAP 176 TLPGMT+VCGDSHT+THGAFGALA GIGTSEVEHVLATQ L + K M++ V+GK Sbjct: 123 ATLPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAKKMKNMQVRVEGKLPF 182 Query: 177 GITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPD 236 G+TAKDIVLA+IGK G+AGG GH +EF G AIRDLSMEGRMT+CNM+IE GA+ G+VA D Sbjct: 183 GVTAKDIVLAVIGKIGTAGGNGHALEFAGSAIRDLSMEGRMTICNMSIEAGARVGMVAVD 242 Query: 237 ETTFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQ 296 E T YV+GR APKG D+D AV W+ L +D+ A FDTVV L+AE+I PQV+WGT+P Sbjct: 243 EKTIAYVEGRPFAPKGDDWDKAVELWQGLVSDDDAVFDTVVELKAEDIKPQVSWGTSPEM 302 Query: 297 VISVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLR 356 V++V+ +PDPA ADPV+R S +AL YMGL P+TE+ +D+VFIGSCTNSRIEDLR Sbjct: 303 VLAVDQKVPDPAVEADPVKRDSIMRALKYMGLNANQPITEIKLDRVFIGSCTNSRIEDLR 362 Query: 357 AAAEIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNN 415 AAAE+AKGRKVA V QALVVPGSG VK QAEAEGLDKIF+EAGFEWR PGCSMCLAMN Sbjct: 363 AAAEVAKGRKVAANVKQALVVPGSGLVKQQAEAEGLDKIFVEAGFEWREPGCSMCLAMNP 422 Query: 416 DRLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465 D+L GE CASTSNRNFEGRQG GGRTHLVSPAMAAAAAVTGHF D+R + Sbjct: 423 DKLGSGEHCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAVTGHFIDVREL 472 Lambda K H 0.317 0.134 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 758 Number of extensions: 20 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 466 Length of database: 475 Length adjustment: 33 Effective length of query: 433 Effective length of database: 442 Effective search space: 191386 Effective search space used: 191386 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate GFF2541 Psest_2591 (3-isopropylmalate dehydratase, large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00170.hmm # target sequence database: /tmp/gapView.24911.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00170 [M=466] Accession: TIGR00170 Description: leuC: 3-isopropylmalate dehydratase, large subunit Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-239 781.1 1.3 2.1e-239 780.7 1.3 1.0 1 lcl|FitnessBrowser__psRCH2:GFF2541 Psest_2591 3-isopropylmalate deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF2541 Psest_2591 3-isopropylmalate dehydratase, large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 780.7 1.3 2.1e-239 2.1e-239 2 466 .] 3 472 .. 2 472 .. 0.98 Alignments for each domain: == domain 1 score: 780.7 bits; conditional E-value: 2.1e-239 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr.....d 71 ktly+kl++ h vk+ +++++l+yidrh++hevtspqafeglr a+rk r+d +at dhn++t++ lcl|FitnessBrowser__psRCH2:GFF2541 3 GKTLYDKLWEMHEVKRRDDGSSLIYIDRHILHEVTSPQAFEGLRLANRKPWRIDANIATPDHNVPTTKGerqggL 77 59***************************************************************9876455543 PP TIGR00170 72 veikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146 i +e++++qv++l++n+++fg+ f +++++qgivhv+gpe+g tlpg+t+vcgdsht+thgafgala gigt lcl|FitnessBrowser__psRCH2:GFF2541 78 EAIADEVSRIQVQTLDENCDDFGILEFKMNDVRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGAFGALAHGIGT 152 46899********************************************************************** PP TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcn 221 sevehvlatq l+ ++ k+++++vegkl g+takdi+la+igkig+agg g+ +efag airdlsme+rmt+cn lcl|FitnessBrowser__psRCH2:GFF2541 153 SEVEHVLATQCLVAKKMKNMQVRVEGKLPFGVTAKDIVLAVIGKIGTAGGNGHALEFAGSAIRDLSMEGRMTICN 227 *************************************************************************** PP TIGR00170 222 maieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgq 296 m+ieaga+ g++a de t++yv +r++apkg++++kav+ w+ l +d++a+fd+vv l+a+di pqv+wgt+p++ lcl|FitnessBrowser__psRCH2:GFF2541 228 MSIEAGARVGMVAVDEKTIAYVEGRPFAPKGDDWDKAVELWQGLVSDDDAVFDTVVELKAEDIKPQVSWGTSPEM 302 *************************************************************************** PP TIGR00170 297 vlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnv 371 vl+v+++vpdp+ adpv++ s+ +al+y+gl++++++++ik+d+vfigsctnsriedlraaaev+kg+kva nv lcl|FitnessBrowser__psRCH2:GFF2541 303 VLAVDQKVPDPAVEADPVKRDSIMRALKYMGLNANQPITEIKLDRVFIGSCTNSRIEDLRAAAEVAKGRKVAANV 377 *************************************************************************** PP TIGR00170 372 klalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlv 446 k+alvvpgsglvk+qae+egldkif+eagfewre+gcs+cl+mn+d+l+++e castsnrnfegrqg+g+rthlv lcl|FitnessBrowser__psRCH2:GFF2541 378 KQALVVPGSGLVKQQAEAEGLDKIFVEAGFEWREPGCSMCLAMNPDKLGSGEHCASTSNRNFEGRQGAGGRTHLV 452 *************************************************************************** PP TIGR00170 447 spamaaaaavagkfvdirel 466 spamaaaaav+g+f+d+rel lcl|FitnessBrowser__psRCH2:GFF2541 453 SPAMAAAAAVTGHFIDVREL 472 ******************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (475 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 11.29 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory